In the 2011-2012, we focused on three major research areas: 1) screening and characterizing drugs that can block malaria transmission; 2) studying parasite molecules and mechanisms of parasite response to antimalarial drugs, particularly artemisinin and derivatives; and 3) studying the molecular mechanism of malaria pathogenesis using Plasmodium yoelii/mouse model. We also finished several smaller projects such as characterizing a new malaria vaccine candidate and analyzing antisense transcripts in different Plasmodium falciparum developmental stages. To identify drugs that can block parasite development in mosquitoes, we disrupted a gene encoding a putative ABC transporter (PfABCG2) that is highly expressed in sexual stages. We then screened parasites with the gene knockout and the wild-type 3D7 parasite against a library of small molecules containing 2,816 drugs approved for human or animal use and identified a compound that was highly potent in blocking oocyst development of P. falciparum and the rodent parasite P. yoelii in mosquitoes. Tests of structurally related compounds also identified additional compounds having similar activities in blocking parasite transmission. Additionally, the compound appeared to have some activity against relapse of Plasmodium cynomolgi in rhesus monkeys. This work has led to a patent application, and a manuscript has been submitted. Following our previous genome-wide association study that identified several candidate genes associated with response to artemisinin and other antimalarial drugs, we now have genetically disrupted a candidate gene and showed that parasites without the gene became more resistant to artemisinin. Further functional characterization and protein localization are being conducted to elucidate the function of the gene and its role in metabolism or resistance of artemisinin. This work can potentially provide important information about the mechanism of artemisinin transport or metabolism within the parasite. We have made good progress in studying parasite-host interactions using rodent malaria parasite P. yoelii. We have screened and compared host responses to infection of different parasite strains and identified differences in host innate immune response, parasite growth, and disease severity. We measured parasitemia over time, mouse mortality, and cytokine/chemokine levels of non-infected and infected mice. We then performed multiple genetic crosses to identify parasite molecules that cause the differences in host response and disease phenotypes. We have identified several genetic loci and candidate genes and are in the process of verifying the functions or the contribution of the candidate genes to the phenotypes. We are also studying the mechanism of host innate immune response to malaria infection. Understanding the molecular mechanism of host-parasite interaction will allow development of effective measures to control parasite development and the disease it causes. To better understand the relationship of gene expression and parasite development, we sequenced seven bidirectional libraries from ring, early and late trophozoite, schizont, gametocyte II, gametocyte V, and ookinete, and four strand-specific libraries from late trophozoite, schizont, gametocyte II, and gametocyte V of the 3D7 P. falciparum parasite. After analysis of the sequences, we identified large numbers of stage-specific antisense transcripts and novel intron-exon splicing junctions. Our results suggested that more genes are expressed in one direction in gametocytes than in schizonts and that antisense RNA may play an important role in gene expression regulation and parasite development. These observations will help us better understand the mechanism of gene expression and regulation in malaria parasites.